Global proteomic analysis of the PINK1-Parkin pathway and elucidation of mitochondrial regulation

• Project/Area Number: 20K06628
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 44010:Cell biology-related
• Research Institution: The University of Tokushima
• Principal Investigator: KOSAKO Hidetaka 徳島大学, 先端酵素学研究所, 教授 (10291171)
• Project Period (FY): 2020-04-01 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2021: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2020: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: プロテオーム / PINK1 / Parkin / ミトコンドリア / パーキンソン病 / 質量分析 / IP-MS / AQUA / 近接ビオチン標識法 / 免疫沈降 / 絶対定量 / オートファジー / ユビキチン化 / nanobody

Outline of Research at the Start

家族性パーキンソン病の原因遺伝子産物であるPINK1とParkinがオートファジーによって不良ミトコンドリアを除去するメカニズムの概要が最近明らかになったが、従来の研究からはその全貌が明らかにされていない。本研究では、最先端のプロテオミクス技術を用いてPINK1-Parkin経路の構成因子を網羅的に同定する。そしてPINK1とParkinの新たな相互作用因子や下流基質の機能を調べることにより、PINK1が如何にしてミトコンドリア異常を検知する分子センサーとして機能するかを明らかにする。さらにParkinがどのような分子をユビキチン化することでミトコンドリア機能を制御するかを明らかにする。

Outline of Final Research Achievements

Recent studies have elucidated the molecular mechanism by which the serine/threonine kinase PINK1 and the ubiquitin ligase Parkin, the causative gene products of familial Parkinson's disease, cooperate to selectively remove damaged mitochondria through autophagy. In this study, we have identified and quantified new interacting proteins with PINK1 and Parkin by proteomic analyses such as immunoprecipitation-mass spectrometry (IP-MS) and targeted mass spectrometry (parallel reaction monitoring: PRM). Our results suggest that TIM23 interacts with PINK1 to prevent degradation of PINK1 by inner membrane proteases in damaged mitochondria.

Academic Significance and Societal Importance of the Research Achievements

PINK1とParkinがオートファジーによってミトコンドリアの品質管理を行う仕組みの概要が最近明らかになったが、従来の細胞生物学や分子生物学を基盤とする研究からは、その全体像を理解する上で十分な知見が得られていなかった。本研究において複数のプロテオーム解析技術を駆使することにより、PINK1とParkinの新たな相互作用因子を多数同定することができた。そしてPINK1との新たな相互作用因子であるTIM23の損傷ミトコンドリアでの機能を明らかにした。

Research Products

• [Journal Article] In vivo CRISPR screening directly targeting testicular cells (2024)
  • Author(s): Noguchi Yuki、Onodera Yasuhito、Miyamoto Tatsuo、Maruoka Masahiro、Kosako Hidetaka、Suzuki Jun
  • Journal Title: Cell Genomics Volume: 4 Issue: 3 Pages: 100510-100510
  • DOI: 10.1016/j.xgen.2024.100510
  • Peer Reviewed / Open Access
• [Journal Article] ALLO-1- and IKKE-1-dependent positive feedback mechanism promotes the initiation of paternal mitochondrial autophagy (2024)
  • Author(s): Sasaki Taeko、Kushida Yasuharu、Norizuki Takuya、Kosako Hidetaka、Sato Ken、Sato Miyuki
  • Journal Title: Nature Communications Volume: 15 Issue: 1 Pages: 1460-1460
  • DOI: 10.1038/s41467-024-45863-2
  • Peer Reviewed / Open Access
• [Journal Article] HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence (2024)
  • Author(s): 1.Cui, M., Yamano, K., Yamamoto, K., Yamamoto-Imoto, H., Minami, S., Yamamoto, T., Matsui, S., Kaminishi, T., Shima, T., Ogura, M., Tsuchiya, M., Nishino, K., Layden B., Kato, H., Ogawa, H., Oki, S., Okada, Y., Isaka, Y., Kosako, H., Matsuda, N., *Yoshimori, T., *Nakamura, S.
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 121 Issue: 2
  • DOI: 10.1073/pnas.2306454120
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Proximity extracellular protein-protein interaction analysis of EGFR using AirID-conjugated fragment of antigen binding (2023)
  • Author(s): Yamada Kohdai、Shioya Ryouhei、Nishino Kohei、Furihata Hirotake、Hijikata Atsushi、Kaneko Mika K.、Kato Yukinari、Shirai Tsuyoshi、Kosako Hidetaka、Sawasaki Tatsuya
  • Journal Title: Nature Communications Volume: 14 Issue: 1 Pages: 8301-8301
  • DOI: 10.1038/s41467-023-43931-7
  • Peer Reviewed / Open Access
• [Journal Article] Extracellular calcium functions as a molecular glue for transmembrane helices to activate the scramblase Xkr4 (2023)
  • Author(s): Zhang Panpan、Maruoka Masahiro、Suzuki Ryo、Katani Hikaru、Dou Yu、Packwood Daniel M.、Kosako Hidetaka、Tanaka Motomu、Suzuki Jun
  • Journal Title: Nature Communications Volume: 14 Issue: 1 Pages: 5592-5592
  • DOI: 10.1038/s41467-023-40934-2
  • Peer Reviewed / Open Access
• [Journal Article] TIM23 facilitates PINK1 activation by safeguarding against OMA1-mediated degradation in damaged mitochondria (2023)
  • Author(s): Shiori Akabane, Kiyona Watanabe, Hidetaka Kosako, Shun-ichi Yamashita, Kohei Nishino, Masahiro Kato, Shiori Sekine, Tomotake Kanki, Noriyuki Matsuda, Toshiya Endo, Toshihiko Oka
  • Journal Title: Cell Reports Volume: 42 Issue: 5 Pages: 112454-112454
  • DOI: 10.1016/j.celrep.2023.112454
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] VGLL3 is a mechanosensitive protein that promotes cardiac fibrosis through liquid-liquid phase separation (2023)
  • Author(s): Horii Yuma、Matsuda Shoichi、Toyota Chikashi、Morinaga Takumi、Nakaya Takeo、Tsuchiya Soken、Ohmuraya Masaki、Hironaka Takanori、Yoshiki Ryo、Kasai Kotaro、Yamauchi Yuto、Takizawa Noburo、Nagasaka Akiomi、Tanaka Akira、Kosako Hidetaka、Nakaya Michio
  • Journal Title: Nature Communications Volume: 14 Issue: 1 Pages: 1-19
  • DOI: 10.1038/s41467-023-36189-6
  • Peer Reviewed / Open Access
• [Journal Article] Binding of LAG-3 to stable peptide-MHC class II limits T?cell function and suppresses autoimmunity and anti-cancer immunity (2022)
  • Author(s): Maruhashi Takumi、Sugiura Daisuke、Okazaki Il-mi、Shimizu Kenji、Maeda Takeo K.、Ikubo Jun、Yoshikawa Harunori、Maenaka Katsumi、Ishimaru Naozumi、Kosako Hidetaka、Takemoto Tatsuya、Okazaki Taku
  • Journal Title: Immunity Volume: - Issue: 5 Pages: 912-924
  • DOI: 10.1016/j.immuni.2022.03.013
  • Peer Reviewed / Open Access
• [Journal Article] Cell cycle-specific phase separation regulated by protein charge blockiness (2022)
  • Author(s): Yamazaki H、Takagi M、Kosako H、Hirano T、Yoshimura SH.
  • Journal Title: Nature Cell Biology Volume: - Issue: 5 Pages: 625-632
  • DOI: 10.1038/s41556-022-00903-1
  • Peer Reviewed / Open Access
• [Journal Article] Optimized Workflow for Enrichment and Identification of Biotinylated Peptides Using Tamavidin 2-REV for BioID and Cell Surface Proteomics (2022)
  • Author(s): Nishino Kohei、Yoshikawa Harunori、Motani Kou、Kosako Hidetaka
  • Journal Title: Journal of Proteome Research Volume: 21 Issue: 9 Pages: 2094-2103
  • DOI: 10.1021/acs.jproteome.2c00130
  • Peer Reviewed
• [Journal Article] The Golgi-resident protein ACBD3 concentrates STING at ER-Golgi contact sites to drive export from the ER (2022)
  • Author(s): Motani Kou、Saito-Tarashima Noriko、Nishino Kohei、Yamauchi Shunya、Minakawa Noriaki、Kosako Hidetaka
  • Journal Title: Cell Reports Volume: 41 Issue: 12 Pages: 111868-111868
  • DOI: 10.1016/j.celrep.2022.111868
  • Peer Reviewed / Open Access
• [Journal Article] Identification and validation of new ERK substrates by phosphoproteomic technologies including Phos-tag SDS-PAGE (2022)
  • Author(s): Yoshikawa Harunori、Nishino Kohei、Kosako Hidetaka
  • Journal Title: Journal of Proteomics Volume: 258 Pages: 104543-104543
  • DOI: 10.1016/j.jprot.2022.104543
  • Peer Reviewed
• [Journal Article] Identification of an endoplasmic reticulum proteostasis modulator that enhances insulin production in pancreatic β cells (2022)
  • Author(s): Miyake Masato、Sobajima Mitsuaki、Kurahashi Kiyoe、Shigenaga Akira、Denda Masaya、Otaka Akira、Saio Tomohide、Sakane Naoki、Kosako Hidetaka、Oyadomari Seiichi
  • Journal Title: Cell Chemical Biology Volume: 7 Issue: 6 Pages: 996-1009
  • DOI: 10.1016/j.chembiol.2022.01.002
  • Peer Reviewed
• [Journal Article] A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues (2022)
  • Author(s): Yamanaka Satoshi、Horiuchi Yuto、Matsuoka Saya、Kido Kohki、Nishino Kohei、Maeno Mayaka、Shibata Norio、Kosako Hidetaka、Sawasaki Tatsuya
  • Journal Title: Nature Communications Volume: 13 Issue: 1 Pages: 183-183
  • DOI: 10.1038/s41467-021-27818-z
  • Peer Reviewed / Open Access
• [Journal Article] Caspase cleavage releases a nuclear protein fragment that stimulates phospholipid scrambling at the plasma membrane (2021)
  • Author(s): Masahiro Maruoka, Panpan Zhang, Hiromi Mori, Eiichi Imanishi, Daniel M Packwood, Hiroshi Harada, Hidetaka Kosako, Jun Suzuki
  • Journal Title: Mol Cell Volume: 81 (7) Issue: 7 Pages: 1397-1410
  • DOI: 10.1016/j.molcel.2021.02.025
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mammalian BCAS3 and C16orf70 associate with the phagophore assembly site in response to selective and non-selective autophagy (2021)
  • Author(s): Kojima W, Yamano K, Kosako H, Imai K, Kikuchi R, Tanaka K, Matsuda N
  • Journal Title: Autophagy Volume: - Issue: 8 Pages: 1-26
  • DOI: 10.1080/15548627.2021.1874133
  • NAID: 120007174412
  • Peer Reviewed / Open Access
• [Journal Article] The ubiquitination-deubiquitination cycle on the ribosomal protein eS7A is crucial for efficient translation (2021)
  • Author(s): Takehara Yuka、Yashiroda Hideki、Matsuo Yoshitaka、Zhao Xian、Kamigaki Akane、Matsuzaki Tetsuo、Kosako Hidetaka、Inada Toshifumi、Murata Shigeo
  • Journal Title: iScience Volume: 24 Issue: 3 Pages: 102145-102145
  • DOI: 10.1016/j.isci.2021.102145
  • NAID: 120007182109
  • Peer Reviewed / Open Access
• [Journal Article] BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING) (2020)
  • Author(s): Motani Kou、Kosako Hidetaka
  • Journal Title: Journal of Biological Chemistry Volume: 295 Issue: 32 Pages: 11174-11183
  • DOI: 10.1074/jbc.ra120.014323
  • NAID: 120007132263
  • Peer Reviewed / Open Access
• [Presentation] 先端プロテオーム解析技術を用いた生体内蛋白質間相互作用の大規模解析 (2022)
  • Author(s): 小迫 英尊
  • Organizer: 第22回日本蛋白質科学会年会
  • Invited
• [Presentation] Global interactome analysis in living cells using advanced proteomic technologies (2021)
  • Author(s): Kosako Hidetaka
  • Organizer: 第44回 日本分子生物学会年会
  • Invited
• [Presentation] 最先端プロテオミクス技術を用いた疾患に関与するシグナル伝達機構の解明 (2020)
  • Author(s): 小迫 英尊
  • Organizer: 第93回日本生化学会大会
  • Invited
• [Remarks] タンパク質分解誘導剤依存的な相互作用解析技術の開発のホームページ
  • URL: https://www.tokushima-u.ac.jp/fs/3/5/6/7/4/0/_/sasikae.pdf